Thermodynamic measures on protein-protein interaction networks for cancer therapy

ABSTRACT

A method to select a protein target for therapeutic application includes accessing genomic information and protein-protein interaction (PPI) data, computing a thermodynamic measure for each protein node within the network of protein nodes, generating an energy landscape data corresponding to the network of protein nodes and the thermodynamic measure, generating a PPI subnetwork by applying a topological filtration to the energy landscape data of the PPI data, computing a first Betti number for the PPI subnetwork, sequentially removing a protein node(s) from the PPI subnetwork while replacing the previously removed nodes(s), computing a new Betti number for the PPI subnetwork with the protein node(s) removed, computing a change between the Betti numbers, and determining, based on the change between the Beti numbers, a most significant protein target within the PPI network.

BACKGROUND

There is an increasing amount of online bioinformatics data (includingbut not limited to a human protein-protein (PPI) network, PPI datagenerally, and transcriptome data) that is not being used by cliniciansfor therapy. The difficulty is that there is too much information andfew relationships between different proteins that have been established.

In a research paper titled “Molecular signaling network complexity iscorrelated with cancer patient survivability” published by Breitkruetzet al. in 2012 in volume 109 issue 23 of the Proceedings of the NationalAcademy of Sciences, it has been established that complexity of cancerprotein-protein interaction (PPI) networks, as measured bydegree-entropy, is strongly correlated with cancer patient survivalstatistics.

Researchers have also suggested that modular bridges and overlaps ofprotein-protein interaction and signaling networks may be of keyimportance in drug design. Social association of nodes, perturbationcentrality, and centrality measures are used to identify important nodesand substrate binding sites and amino acids participating in allostericsignaling in protein structure networks.

SUMMARY

A computer-implemented method to select a protein target for therapeuticapplication including the steps of accessing genomic information andprotein-protein interaction (PPI) data, the PPI data comprising anetwork of protein nodes from at least one source, computing, using thegenomic information and the PPI data, a thermodynamic measure for eachprotein node within the network of protein nodes, generating an energylandscape data corresponding to the network of protein nodes and thethermodynamic measure, generating a PPI subnetwork by applying atopological filtration to the energy landscape data of the PPI data,computing a first Betti number for the PPI subnetwork, sequentiallyremoving a first protein node from the PPI subnetwork, computing asecond Betti number for the PPI subnetwork with the first protein noderemoved, computing a change between the first Betti number and thesecond Betti number, replacing the first protein node into the PPIsubnetwork, sequentially removing a second protein node from the PPIsubnetwork, wherein the second protein node is different from the firstprotein node, computing a third Betti number for the PPI subnetwork withthe second protein node removed and the first protein node replaced,computing a change between the first Betti number and the third Bettinumber, and determining, based on the change between the first Bettinumber and the second Betti number and the change between the firstBetti number and the third Betti number, a most significant proteintarget within the PPI subnetwork.

A computing system that selects a protein target for therapeuticapplication, including a processing circuitry configured to executeinstructions to: access genomic information and protein-proteininteraction (PPI) data comprising a network of protein nodes from atleast one source, compute, using the genomic information and the PPIdata, a thermodynamic measure for each of the protein nodes within thenetwork, generate an energy landscape data corresponding to the networkand the thermodynamic measure, generate a PPI subnetwork by applying atopological filtration to the energy landscape of the PPI data, computea first Betti number for the PPI subnetwork, sequentially remove a firstprotein node from the PPI subnetwork, compute a second Betti number forthe PPI subnetwork with the first protein node removed, compute a changebetween the first Betti number and the second Betti number, replace thefirst protein node into the PPI subnetwork, sequentially remove a secondprotein node different from the first protein node from the PPIsubnetwork, compute a third Betti number for the PPI subnetwork with thesecond protein node removed and first protein node replaced, compute achange between the first Betti number and the third Betti number, anddetermine, based on the change between the first Betti number and thesecond Betti number and the change between the first Betti number andthe third Betti number, a most significant protein target within the PPIsubnetwork, and a display circuitry configured to execute instructionsto display the most significant protein target to a user.

A non-transitory computer-readable medium having instructions storedthereon that, in response to execution by the computer system, cause thecomputer system to perform operations including: computing, using thegenomic information and the PPI data, a thermodynamic measure for eachof the protein nodes within the network, generating an energy landscapedata corresponding to the network and the thermodynamic measure,generating a PPI subnetwork by applying a topological filtration to theenergy landscape of the PPI data, computing a first Betti number for thePPI subnetwork, sequentially removing a first protein node from the PPIsubnetwork, computing a second Betti number for the PPI subnetwork withthe first protein node removed, computing a change between the firstBetti number and the second Betti number, replacing the first proteinnode into the PPI subnetwork, sequentially removing a second proteinnode different from the first protein node from the PPI subnetwork,computing a third Betti number for the PPI subnetwork with the secondprotein node removed and first protein node replaced, computing a changebetween the first Betti number and the third Betti number, determining,based on the change between the first Betti number and the second Bettinumber and the change between the first Betti number and the third Bettinumber, a most significant protein target within the PPI subnetwork.

Other aspects and advantages of the invention will be apparent from thefollowing description and the appended claims.

BRIEF DESCRIPTION OF DRAWINGS

FIGS. 1, 2, and 3 show a graph in accordance with one or moreembodiments.

FIG. 4 shows diagrams in accordance with one or more embodiments.

FIGS. 5A, 5B, 5C, and 5D show diagrams in accordance with one or moreembodiments.

FIGS. 6A and 6B show a graph in accordance with one or more embodiments.

FIGS. 7, 8, and 9 show a graph in accordance with one or moreembodiments.

FIGS. 10A and 10B show a computing system in accordance with one or moreembodiments.

FIG. 11 shows a schematic diagram in accordance with one or moreembodiments.

FIGS. 12A and 12B show a flowchart in accordance with one or moreembodiments.

DETAILED DESCRIPTION

While the invention has been described with respect to a limited numberof embodiments, those skilled in the art, having benefit of thisdisclosure, will appreciate that other embodiments can be devised whichdo not depart from the scope of the invention as disclosed herein.Accordingly, the scope of the invention should be limited only by theattached claims.

Throughout the application, ordinal numbers (e.g., first, second, third,etc.) may be used as an adjective for an element (i.e., any noun in theapplication). The use of ordinal numbers does not imply or create aparticular ordering of the elements nor limit any element to being onlya single element unless expressly disclosed, such as by the use of theterms “before,” “after,” “single,” and other such terminology. Rather,the use of ordinal numbers is to distinguish between the elements. Byway of an example, a first element is distinct from a second element,and the first element may encompass more than one element and succeed(or precede) the second element in an ordering of elements.

It is to be understood that the singular forms “a,” “an,” and “the”include plural referents unless the context clearly dictates otherwise.Thus, for example, reference to “a horizontal beam” includes referenceto one or more of such beams.

Terms like “approximately,” “substantially,” etc., mean that the recitedcharacteristic, parameter, or value need not be achieved exactly, butthat deviations or variations, including for example, tolerances,measurement error, measurement accuracy limitations and other factorsknown to those of skill in the art, may occur in amounts that do notpreclude the effect the characteristic was intended to provide.

Although multiple dependent claims are not introduced, it would beapparent to one of ordinary skill in that that the subject matter of thedependent claims of one or more embodiments may be combined with otherdependent claims. For example, even though claim 3 does not directlydepend from claim 2, even if claim 2 were incorporated into independentclaim 1, claim 3 is still able to be combined with independent claim 1that would now recite the subject matter of dependent claim 2.

In one or more embodiments, a thermodynamic measure is described thatallows mapping the molecular pathway, also referred to as the molecularsubnetwork or PPI subnetwork, for each patient at each stage of thecancer progression. This allows selection of molecular targets fortreatment with a high confidence that the targets have significantmeaning for that patient.

In general, embodiments of the invention describe a linear correlationof Gibbs free energy and cancer patient survival. In one or moreembodiments, the Gibbs free energy persistent homology on each cancerPPI network is calculated for each patient. Furthermore, the relevantenergetic molecular subnetwork, from which another topological measureto compute the Betti (or cycle-basis) number is used, is obtained toselect protein targets for inhibition. Because there is a linearcorrelation with Gibbs free energy, these targets can be selected withconfidence.

For example, based on the genetic and phenotypic background of anindividual, a different proliferative subnetwork may be engaged in tumorgrowth. In most cancers, more than one genomic and proteomic alterationis usually identified, resulting in a disadvantage situation where theimportance of one molecular alteration over another molecular alterationcannot be easily determined.

An advantage achieved by one or more embodiments compared toconventional therapy is the high confidence for selecting a molecularalteration, also referred to as the most significant target protein(s),that causes the largest effect on the subnetwork when inhibited. Itwould apparent to one of ordinary skill in the art that the molecularalteration that causes the largest effect on the subnetwork would havethe largest impact on inhibiting the progression of the cancer.

In general, the phrase “the most significant protein target(s)” isdefined as the protein node(s) in a network or subnetwork that causesthe largest change in Betti number when removed. In other words the“most significant” protein target(s) is the number one protein target(s)of choice when administering drugs during therapy.

The following examples and description are for explanatory purposes onlyand not intended to limit the scope of the invention.

The homeostasis of cells is maintained by a complex, dynamic network ofinteracting molecules ranging in size from a few dozen Daltons tohundreds of thousands of Daltons. Any change in concentration of one ormore of these molecular species alters the chemical balance, or in termsof thermodynamics, chemical potential. These changes then percolatethrough the network affecting the chemical potential of other species.The end result is perturbations in the network manifesting asconcentration changes, giving rise to changes in the energetic landscapeof the cell. In the Third Edition of “Physical Chemistry” published byW.H. Freeman and Company in 1986 and in the “Introduction to TheoreticalOrganic Chemistry” published by Macmillan Company in 1968, authors P. W.Atkins and A. Liberles, respectively, describe these energetic changesas chemical potential on an energetic landscape.

Gene alterations (mutations, variations in expression, translocations,etc.) invariably alter the chemical potential of one or more proteinsand/or other molecular species within a single cell. Yet, twoneighboring cancer cells in the same microenvironment may exhibit adifferent energetic landscape because the chemical potential isdifferent within the two cells. Naturally, when a bundle of cells areharvested, for example in a biopsy, and the cells are digested toextract RNA for transcription analysis, the transcriptome is essentiallyan average of that bundle of cells. Since genes code for proteins, thetranscriptome can act as a surrogate for the concentration of theproteins.

To support the conjecture described above, a 2013 publication byGreenbaum et al. on page 117 of volume 4 of Genome Biology titled“Comparing protein abundance and mRNA expression levels on a genomicscale” and a 2009 publication by Maier et al. in pages 3966 to 3973 ofvolume 583 of the FEBS Letters titled “Correlation of mRNA and proteinin complex biological samples,” have described correlations of mRNA withprotein concentrations and found Pearson correlation, R, to range from0.4 to 0.8, in a large number of experiments across five differentspecies. Similarly, as described in a publication titled“Mass-spectrometry-based draft of the human proteome” in pages 582 to587 of volume 509 of Nature, Wilhelm et al. conducted an extensive studyon human tissues using both proteomic and mRNA expression and foundroughly an 86% correlation between expression and protein concentration.

Data for several cancers from The Cancer Genome Atlas (TCGA) hosted bythe National Institute of Health (www.cancergnome.nih.gov) have beencollected. The Cancer Genome Atlas is described by The TGCA ResearchNetwork publications in the journal, Nature. A set of data that used theAgilent platform G4502A has also been collected and was pre-collapsed ongene symbols. Further, a total of eleven cancers were collected from thefollowing sources: KIRC (kidney renal clear cell) from a 2013publication by The TGCA Research Network titled “Comprehensive molecularcharacterizations of clear cell renal cell carcinoma,” published inpages 43 to 49 of volume 499 of Nature; KIRP (kidney renal papillarycell); LGG (low grade glioma); GBM (glioblastoma multiforme) from a 2008publication by The TGCA Research Network titled “Comprehensive geneticcharacterization defines human glioblastoma genes and core pathways,”published in page 1061 of volume 455 of Nature; COAD (coloinadenocarcinoma) from a 2012 publication by The TGCA Research Networktitled “Comprehensive molecular characterization of human colon andrectal cancer,” published in pages 330 to 337 of volume 487 of Nature;BRCA (breast invasive carcinoma) from a 2012 publication by The TGCAResearch Network titled “Comprehensive molecular portraits of humanbreast tumors,” published in pages 61 to 70 of volume 490 of Nature;LUAD (lung adenocarcinoma); LUSC (lung squamous cell) from a 2012publication by The TGCA Research Network titled “Comprehensive genomiccharacterization of squamous cell lung cancers,” published in pages 519to 525 of volume 489 of Nature; UCEC (uterine corpus endometrial) from a2013 publication by The TGCA Research Network titled “Integrated genomiccharacterization of endometrial carcinoma,” published in pages 67 to 73of volume 497 of Nature; OV (ovarian serous cystadenocarcinoma) from a2012 publication by The TGCA Research Network titled “Integrated genomicanalysis of ovarian carcinoma,” published in pages 609 to 615 of volume476 of Nature; READ (rectum adenocarcinoma).

In one or more embodiments, two databases for survival data are used.The first database is the Surveillance Epidemiology and End Results(SEER) National Cancer Institute database, which contains detailedstatistical information about the five-year survival rates of patientswith cancer. The second database is the National Brain tumor Societydatabase. While these two databases may be used, a single database ormultiple other databases could be used that provide the same orequivalent data.

FIG. 1 shows a graph in accordance to one or more embodiments. In one ormore embodiments, FIG. 1 shows the application of the TCGA datadescribed above. As seen in FIG. 1 , the 5 year survival rate andcorrelating Gibbs free energy number for the different cancers:glioblastoma multiforme (GMB) (100), lung adenocarcinoma (LUAD) (102),rectum adenocarcinoma (READ) (104), colon adenocarcinoma (COAD) (106),uterine corpis endometrial (UCEC) (108), lung squamous cell (LUSC)(110), ovarian serous cystadenocarcinoma (OV) (112), low grade glioma(LGG) (114), and breast invasive glioma (BRCA) (116) are plotted. They-axis in FIG. 1 is the Gibbs energy shown in an arbitrary scale and thex-axis represents the probability of 5-year patent survival.

As seen in FIG. 1 , a linear correlation (116) exists between overallGibbs free energy and 5-year survival rate. This result demonstratesthat the probability of 5-year patient survival is inverselyproportional to the complexity of the signaling network (measured byGibbs energy) for the types of cancer considered. Other measures ofnetwork complexity, such as degree-entropy, number of leaf nodes, and/orcyclomatic number have also been found to inversely correlate with 5year survival. These results indicate the existence of a correlationbetween the probability of survival (clinical data) and the complexityof signaling networks (mathematical inference). Furthermore, theseresults also imply that the inactivation of certain protein targets(e.g. those that can reduce network complexity) can bring aboutreduction in cancerous growth and increase in survival.

FIG. 2 shows a graph in accordance with one or more embodiments. In oneor more embodiments, FIG. 2 is a graph that shows the Gibbs free energycorrelation with cancer stage for liver cancer. As shown in FIG. 2 , thecancer stages: normal tissue (202), cirrhotic stage (204), low-gradedysplastic (206), high-grade dysplastic (208), early HCC (210), andadvanced HCC (212) are assigned to an ordinal number of 1 through 6 andplotted on the x-axis. In FIG. 2 , the y-axis is the Gibbs energy on anarbitrary scale In FIG. 2 gene expression data from GSE6764 (publicallyavailable) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6764)was normalized so as to be in the range of [0,1] and overlaid on aprotein-protein interaction network from Biogrid® using Gibbs freeenergy equations described later in one or more embodiments. In FIG. 2 ,the Pearson correlation is −0.927, the Spearman correlation of the meanGibbs free energy for the individual cancer stages is R=−0.99 with ap-value of 0.0001, and the Kendall's tau correlation is 1.000, with ap-value of 0.0016.

As seen in FIG. 2 , a linear correlation (214) exists between the Gibbsfree energy and the cancer stages when the cancer stages are assigned toan ordinal number. While other protein-protein interaction networkmeasures may have been found to correlate with survival, the finding ofa linear correlation between Gibbs energy and cancer stage as shown inFIG. 2 is a new discovery. The results in FIG. 2 provides an additionallevel of reassurance that changes in network complexity are relevant tocancer progression, because the complexity of each cancer specificprotein interaction network can be described by quantifying the energyof the connections within the protein interactions. Therefore, if adecrease in network complexity can be correlated with lower cancerstage, then the identification of nodes (proteins) which producesignificant reduction in network complexity can pinpoint the mostappropriate therapeutic target.

In one or more embodiments, the Gene Expression Omnibus (GEO) atwww.ncbi.nlm.nih.gov is accessed for transcription data relevant toprostate and liver carcinoma. The data for the liver cancer study(hepatocellular carcinoma) was GSE6764, and the prostate study GSE3933and GSE6099. The GSE3933 and GSE6099, as obtained, were log(2) processedand collapsed to gene IDs. The data was modified to gene cluster text(.get) file format and processed with GenePattern® at Broad Institute.The expression data for liver cancer, GSE6764, was in an Affymetrix®format (HG_U133_Plus_2 probe set), and also preprocessed to collapsethem into gene IDs.

Similarly, FIG. 3 shows a graph in accordance with one or moreembodiments. In one or more embodiments, FIG. 3 is a graph showing theGibbs energy correlating with cancer stage, more specifically, Gibbsfree energy vs. cancer stage for prostate cancer. As shown in FIG. 3 ,the prostate cancer stages: normal benign prostate hypoplasia (BPH)(302), prostatic interepithelial neoplasia (PIN) (304), primary tmor(Primary) (306), and metastatic (MET) (308) are assigned to an ordinalnumber of 1 through 4 and plotted on the x-axis. In FIG. 3 , the y-axisis the Gibbs energy on an arbitrary scale. In one or more embodiments,for the calculation of FIG. 3 gene expression data from GSE3933 andGSE6099 were normalized so as to be in the range of [0,1] and overlaidon Biogrid® protein-protein interaction network using Gibbs free energyequations described later in one or more embodiments. In FIG. 3 , theSpearman R correlation is −1.000 with p-value.

As seen in FIG. 3 , a linear correlation (310) exists between the Gibbsfree energy and the cancer stages when the cancer stages are assigned toan ordinal number. As described above in FIG. 2 , the identification ofprotein hubs that most contribute to network complexity (most energeticnodes) is likely to pinpoint putative molecular targets for therapy.Carefully choosing a minimum set of protein targets to be inhibited,according to the subnetwork energy, can result in a X % decrease in thecalculated network complexity (measured by Gibbs energy), and can doublethe predicted rate of 5-year survival or reduce cancer stage.

It would be apparent to one of ordinary skill in the art that given thatthe data for these calculations come from such diverse sources it ishighly suggestive that the correlations are good. This suggestsexploiting the Gibbs energy concept for target selection.

FIG. 4 shows diagrams in accordance with one or more embodiments. In oneor more embodiments, once a Gibbs free energy is assigned to each nodein a PPI network, the PPI network can then be viewed as a ruggedlandscape (402) within, for example, a graphical user interface (GUI)(401) as depicted in FIG. 4 . In one or more embodiments of theinvention, the GUI and one or more display devices for viewing the GUIis shown and described in relation to FIG. 10A. Returning to FIG. 4 ,the network with real numbers attached to each node is isomorphic to anenergy landscape (404), which in one or more embodiments is displayedwithin the GUI (401). A topological “filtration” technique can beapplied to the energy landscape (404) to extract a “persistenthomology.”

In one or more embodiments, the human PPI network (Homo sapiens, 3.3.99,March, 2013) from BioGrid (www.thebiogrid.org), which contains 9561nodes and 43,086 edges, was used. The entire human PPI was loaded intoversion 2.8.1 of Cytoscape. In a publication by Shannon et al. titled“Cytoscape: A softward environment for integrated models of bimolecularinteraction networks,” published in 2013 in pages 2498 to 2504 of volume13 issue 11 of Genome Research, Shannon et al. describes the generalapplication and use of the Cytoscape software. The list of genesobtained from TCGA (full-length expression set was 17,814 genes) for aspecific cancer was “selected” using the Cytoscape functions, the“inverse selection” of Cytoscape function applied, and the nodes andgenes edges were removed. The resulting network, which now included onlythose genes found in both Biogrid and TCGA, consisted of 7951 nodes and36,509 edges. This Cytoscape network was unloaded as an adjacency listfor processing by custom Python code using version 2.6.4 of Python withappropriate NetworkX functions.

In one or more embodiments the RNA (e.g., mRNA, rRNA, tRNA, and othernon-coding RNA) transcriptome value as a surrogate for proteinconcentration can be “overlaid” on a PPI network, such as the human PPIat Biogrid (www.biogrid.org) shown as the rugged landscape (402) in FIG.4 . Once the RNA transcriptome value has been overlaid, the log(2)transformed transcription data is first resealed to be in the range[0,1]. In one or more embodiments, the most highly, positively expressedvalue will be set to 1.0 and the most negatively, down-regulated valuewill be set to 0.

It would be apparent to one of ordinary skill in the art that this iscomparable to stating that the most strongly up-regulated gene producesa protein of very great concentration, relative to the most stronglydown-regulated gene that will result in the lowest proteinconcentration.

In one or more embodiments, the corresponding rescaled transcriptomedata is assigned to each protein in the PPI network. The followingequation is then used to compute the Gibbs free energy for that protein:

$\begin{matrix}{G_{i} = {c_{i}\ln\frac{c_{i}}{\sum\limits_{j = i}c_{j}}}} & {{Eq}.\lbrack 1\rbrack}\end{matrix}$

In one or more embodiments, it is assumed that the protein of interestis i with concentration, ci. This concentration is the resealedtranscription data for that gene. In the denominator of the argument tothe natural logarithm the summation is taken over concentrations(resealed) for all the neighbors to the protein of interest, i. This isessentially the Gibbs free energy, Gi, for that protein in the PPInetwork.

In one or more embodiments, the overall Gibbs free energy of the PPInetwork can be obtained using the equation of:

$\begin{matrix}{{qG} = {\sum\limits_{i}G_{i}}} & {{Eq}.\lbrack 2\rbrack}\end{matrix}$

In one or more embodiments, Equation [2] represents the Gibbs freeenergy for a patient. In one or more embodiments, Equation [2] may alsorepresent the different cancer stages for patients, depending on whenthe biopsy was taken.

FIGS. 5A, 5B, 5C, and 5D show diagrams in accordance with one or moreembodiments. In one or more embodiments, shown in FIG. 5A, an energylandscape (404) is shown. In one or more embodiments, shown in FIG. 5B,a topological filtration (502), also referred to as a filtrationthreshold, can be moved up from far below the lowest minima on an energylandscape (404). As the filtration threshold is moved up further, smallconnected subnetworks (504) as shown in FIG. 5D, and later largerconnected subnetworks (506) as shown in FIG. 5C are revealed. Thesesubnetworks are known as persistent homology.

As shown in FIGS. 5C and 5D, it would be apparent to one of ordinaryskill in the art that as the filtration threshold is increased, thecomplexity of the subnetwork is also increased.

In one or more embodiments, if the normalized or rescaled, expressiondata were assigned as real numbers a persistent homology cannot beobtained when the topological filtration is applied. The nodes will bedisconnected until a threshold of several hundred. In contrast, by usingthe normalized or resealed, expression data, a threshold as low as 5 andas high as 7000 gives a smooth change in network measure on thesubnetworks.

FIGS. 6A and 6B shows a graph in accordance with one or moreembodiments. In one or more embodiments, the graph in FIG. 6A shows thecluster coefficient and the graph in FIG. 6B shows the cluster size ofthe persistent homology subnetworks as a functions of the filtrationthreshold. As shown in the first curve (602) in FIG. 6A and the secondcurve (604) in FIG. 6B, no apparent kinks are shown that would representa phase transition as the filtration threshold is increased from 1 to7000.

In one or more embodiments, to demonstrate how the subnetworks are usedfor targeting and treatment of individual patients, the TCGAglioblastoma multiforme (GBM) data is used as an example.

In one or more embodiments, TABLE 1 found below shows a histogram for anetwork metric known as closeness centrality, which measures the meandistance from a node in the network to all other nodes, on 483 GBMpatients. The Gibbs energy persistent homology for the individualpatient was first computed, and the closeness centrality for subnetworksat a filtration threshold of 15 was then computed. In one or moreembodiments, the histogram in Table I shows the full range of closenesscentrality and thus the differences in subnetworks for each patient.

As shown in TABLE 1, the graph in the center presents the distributionof closeness-centrality (the x-axis) vs. the number of subnetworks at afiltration threshold of 15 (the y-axis). On the left of the graph, alist of genes with the respective subnetwork is provided. Thissubnetwork represents an example of the least connected network (e.g.one that has the lowest closeness-centrality of the population ofgraphs). On the right of the graph, another list of genes with therespective subnetwork is provided. In contrast to the list of genes onthe left, the list of genes provided on the right contains the mostconnected network (e.g. the highest closeness-centrality of thepopulation of graphs).

In one or more embodiments, the distribution study as shown in TABLE 1refers to a population of patients and therefore identifies frequency ofspecific homology subnetworks within a population of patients withspecific type of cancer and guide drug treatment for the majority ofpatients vs rare molecular subtypes.

In one or more embodiments, the subnetworks can be used to compute drugtargets. First, the Gibbs energy of the subnetwork is demonstrated assignificant, in relation to survival of GBM patients. In one or moreembodiments, a Cox proportional hazards (Cox PH) model is used to showthis significance.

The Cox proportional hazards is described by Cox in a 1972 publicationtitled “Regression Models and Life Tables” in pages 187 to 220 in seriesB, volume 34, No. 2 of the Journal of Royal Statistical Society.

In a research paper titled “Molecular signaling network complexity iscorrelated with cancer patient survivability” published in 2012 involume 109 issue 23 of the Proceedings of the National Academy ofSciences, Breitkruetz et al. shows that the model was constructed fromseveral statistical and thermodynamic measures on the Gibbs subnetworkat threshold of 32. The statistical measures included: number of edges,transitivity, and clique.

Furthermore, a topological measure known as the Betti number is used.The Betti number is described by Benzekry et al. in a publication titled“Design Principles for Cancer Therapy guided by changes in complexity ofProtein-Protein Interaction Networks.” The Betti number calculates thenumber of rings of four or more nodes in the PPI network, in this casethe Gibbs homology subnetworks.

These six parameters (i.e. number of edges, transitivity, clique,degree-entropy, Betti number, Gibbs energy of the subnetwork) are fittedinto the Cox PH model. The Chi Square probability for the overall modelis 0.0426 and the most important parameter is the Gibbs energy of thesubnetwork with a Chi Square fitting probability of 0.0026. Furthermore,fitting only to days-to-death with gibbs-subnetwork energy inlog-logistic model, a Chi square of <0.0001 is obtained.

In one or more embodiments, the Betti number and the Gibbs energy forthis subnetwork is calculated. It would be apparent that since Bettinumber and Gibbs free energy correlates linearly with survival fordifferent cancers, it is possible to inhibit a protein at differentstages of the cancer that gives the largest drop in Betti number withhigh confidence that the complexity of the subnetwork has been reduced.

In one or more embodiments, whether or not the complexity has beenreduced can be double checked to see if the Gibbs free energy hasincrease. In one or more embodiments, this is done on apatient-to-patient basis. It would be apparent to one of ordinary skillin the art that the method of one or more embodiments, referred to asthe Gibbs-Betti method, can generate an energetic subnetwork for eachpatient no matter the cancer stage. Furthermore, the gibbs-betti methodof one or more embodiments can be used to identify a specific drugtarget for each patient.

FIG. 7 shows a graph according to one or more embodiments. In one ormore embodiments, FIG. 7 shows a hazard model: a fit of days-to-deathwith Gibbs energy for the homology subnetworks at threshold 32 forglioblastoma (using the same TCGA data), which is also referred to as alog-logistic fit. The lowest curve (702) represents the untreatedpatients, and the upper curve (704) is a simulation of patients treatedwith targeted agents that inhibit the proteins identified using theGibbs-homology (threshold 32) and Betti number method as described abovein one or more embodiments. The x-axis represents number of days todeath (from TCGA), and the y-axis is survival fraction (or probabilityof survival).

From the results shown in the graph of one or more embodiments in FIG. 7, it would be apparent to one of ordinary skill in the art that thepatients treated with the Gibbs-Betti method of one or more embodimentssurvived longer than the conventionally treated patients.

FIG. 8 shows a graph according to one or more embodiments. As seen inFIG. 8 , the log-logistic for glioblastoma patients as shown in FIG. 7treated with conventional therapy (802) and glioblastoma patients with asimulated treatment based on the Gibbs-Betti method (804) of one or moreembodiments are compared. The overall improvement of the Gibbs-Bettimethod (804) of one or more embodiments compared to the results forconventional therapy (802) is estimated at 134%.

FIG. 9 shows a graph in accordance with one or more embodiments. FIG. 9shows a Pareto chart (902) of the best targets for individual patients(904) with glioblastoma carcinoma. The chart shows that the best proteintarget among the plurality of protein targets (906) was NCOR1 for 56patients. The chart also shows that MDF1 was the best target for 48patients.

FIGS. 10A and 10B show a computing system in accordance with one or moreembodiments of the technology.

Embodiments of the invention may be implemented on a computing system.Any combination of mobile, desktop, server, router, switch, embeddeddevice, or other types of hardware may be used. For example, as shown inFIG. 10A, the computing system (1000) may include one or more computerprocessors (1002), non-persistent storage (1004) (e.g., volatile memory,such as random access memory (RAM), cache memory), persistent storage(1006) (e.g., a hard disk, an optical drive such as a compact disk (CD)drive or digital versatile disk (DVD) drive, a flash memory, etc.), acommunication interface (1012) (e.g., Bluetooth interface, infraredinterface, network interface, optical interface, etc.), and numerousother elements and functionalities.

The computer processor(s) (1002) may be an integrated circuit forprocessing instructions. For example, the computer processor(s) may beone or more cores or micro-cores of a processor. The computing system(1000) may also include one or more input devices (1010), such as atouchscreen, keyboard, mouse, microphone, touchpad, electronic pen, orany other type of input device.

The communication interface (1012) may include an integrated circuit forconnecting the computing system (1000) to a network (not shown) (e.g., alocal area network (LAN), a wide area network (WAN) such as theInternet, mobile network, or any other type of network) and/or toanother device, such as another computing device.

Further, the computing system (1000) may include one or more outputdevices (1008), such as a screen (e.g., a liquid crystal display (LCD),a plasma display, touchscreen, cathode ray tube (CRT) monitor,projector, or other display device), a printer, external storage, or anyother output device. One or more of the output devices may be the sameor different from the input device(s). The input and output device(s)may be locally or remotely connected to the computer processor(s)(1002), non-persistent storage (1004), and persistent storage (1006).Many different types of computing systems exist, and the aforementionedinput and output device(s) may take other forms.

Software instructions in the form of computer readable program code toperform embodiments of the invention may be stored, in whole or in part,temporarily or permanently, on a non-transitory computer readable mediumsuch as a CD, DVD, storage device, a diskette, a tape, flash memory,physical memory, or any other computer readable storage medium.Specifically, the software instructions may correspond to computerreadable program code that, when executed by a processor(s), isconfigured to perform one or more embodiments of the invention.

The computing system (1000) in FIG. 10A may be connected to or be a partof a network. For example, as shown in FIG. 10B, the network (1020) mayinclude multiple nodes (e.g., node X (1022), node Y (1024)). Each nodemay correspond to a computing system, such as the computing system shownin FIG. 10A, or a group of nodes combined may correspond to thecomputing system shown in FIG. 10A. By way of an example, embodiments ofthe invention may be implemented on a node of a distributed system thatis connected to other nodes. By way of another example, embodiments ofthe invention may be implemented on a distributed computing systemhaving multiple nodes, where each portion of the invention may belocated on a different node within the distributed computing system.Further, one or more elements of the aforementioned computing system(1000) may be located at a remote location and connected to the otherelements over a network.

Although not shown in FIG. 10B, the node may correspond to a blade in aserver chassis that is connected to other nodes via a backplane. By wayof another example, the node may correspond to a server in a datacenter. By way of another example, the node may correspond to a computerprocessor or micro-core of a computer processor with shared memoryand/or resources.

The nodes (e.g., node X (1022), node Y (1024)) in the network (1020) maybe configured to provide services for a client device (1026). Forexample, the nodes may be part of a cloud computing system. The nodesmay include functionality to receive requests from the client device(1026) and transmit responses to the client device (1026). The clientdevice (1026) may be a computing system, such as the computing systemshown in FIG. 10A. Further, the client device (1026) may include and/orperform all or a portion of one or more embodiments of the invention.

The computing system or group of computing systems described in FIGS.10A and JOB may include functionality to perform a variety of operationsdisclosed herein. For example, the computing system(s) may performcommunication between processes on the same or different system. Avariety of mechanisms, employing some form of active or passivecommunication, may facilitate the exchange of data between processes onthe same device. Examples representative of these inter-processcommunications include, but are not limited to, the implementation of afile, a signal, a socket, a message queue, a pipeline, a semaphore,shared memory, message passing, and a memory-mapped file. Furtherdetails pertaining to a couple of these non-limiting examples areprovided below.

Based on the client-server networking model, sockets may serve asinterfaces or communication channel end-points enabling bidirectionaldata transfer between processes on the same device. Foremost, followingthe client-server networking model, a server process (e.g., a processthat provides data) may create a first socket object. Next, the serverprocess binds the first socket object, thereby associating the firstsocket object with a unique name and/or address. After creating andbinding the first socket object, the server process then waits andlistens for incoming connection requests from one or more clientprocesses (e.g., processes that seek data). At this point, when a clientprocess wishes to obtain data from a server process, the client processstarts by creating a second socket object. The client process thenproceeds to generate a connection request that includes at least thesecond socket object and the unique name and/or address associated withthe first socket object. The client process then transmits theconnection request to the server process. Depending on availability, theserver process may accept the connection request, establishing acommunication channel with the client process, or the server process,busy in handling other operations, may queue the connection request in abuffer until server process is ready. An established connection informsthe client process that communications may commence. In response, theclient process may generate a data request specifying the data that theclient process wishes to obtain. The data request is subsequentlytransmitted to the server process. Upon receiving the data request, theserver process analyzes the request and gathers the requested data.Finally, the server process then generates a reply including at leastthe requested data and transmits the reply to the client process. Thedata may be transferred, more commonly, as datagrams or a stream ofcharacters (e.g., bytes).

Shared memory refers to the allocation of virtual memory space in orderto substantiate a mechanism for which data may be communicated and/oraccessed by multiple processes. In implementing shared memory, aninitializing process first creates a shareable segment in persistent ornon-persistent storage. Post creation, the initializing process thenmounts the shareable segment, subsequently mapping the shareable segmentinto the address space associated with the initializing process.Following the mounting, the initializing process proceeds to identifyand grant access permission to one or more authorized processes that mayalso write and read data to and from the shareable segment. Changes madeto the data in the shareable segment by one process may immediatelyaffect other processes, which are also linked to the shareable segment.Further, when one of the authorized processes accesses the shareablesegment, the shareable segment maps to the address space of thatauthorized process. Often. only one authorized process may mount theshareable segment, other than the initializing process, at any giventime.

Other techniques may be used to share data, such as the various datadescribed in the present application, between processes withoutdeparting from the scope of the invention. The processes may be part ofthe same or different application and may execute on the same ordifferent computing system.

Rather than or in addition to sharing data between processes, thecomputing system performing one or more embodiments of the invention mayinclude functionality to receive data from a user. For example, in oneor more embodiments, a user may submit data via a GUI on the userdevice. Data may be submitted via the graphical user interface by a userselecting one or more graphical user interface widgets or inserting textand other data into graphical user interface widgets using a touchpad, akeyboard, a mouse, or any other input device. In response to selecting aparticular item, information regarding the particular item may beobtained from persistent or non-persistent storage by the computerprocessor. Upon selection of the item by the user, the contents of theobtained data regarding the particular item may be displayed on the userdevice in response to the user's selection.

By way of another example, a request to obtain data regarding theparticular item may be sent to a server operatively connected to theuser device through a network. For example, the user may select auniform resource locator (URL) link within a web client of the userdevice, thereby initiating a Hypertext Transfer Protocol (HTTP) or otherprotocol request being sent to the network host associated with the URL.In response to the request, the server may extract the data regardingthe particular selected item and send the data to the device thatinitiated the request. Once the user device has received the dataregarding the particular item, the contents of the received dataregarding the particular item may be displayed on the user device inresponse to the user's selection. Further to the above example, the datareceived from the server after selecting the URL link may provide a webpage in Hyper Text Markup Language (HTML) that may be rendered by theweb client and displayed on the user device.

Once data is obtained, such as by using techniques described above orfrom storage, the computing system, in performing one or moreembodiments of the invention, may extract one or more data items fromthe obtained data. For example, the extraction may be performed asfollows by the computing system in FIG. 10A. First, the organizingpattern (e.g., grammar, schema, layout) of the data is determined, whichmay be based on one or more of the following: position (e.g., bit orcolumn position. Nth token in a data stream, etc.), attribute (where theattribute is associated with one or more values), or a hierarchical/treestructure (consisting of layers of nodes at different levels ofdetail-such as in nested packet headers or nested document sections).Then, the raw, unprocessed stream of data symbols is parsed, in thecontext of the organizing pattern, into a stream (or layered structure)of tokens (where each token may have an associated token “type”).

Next, extraction criteria are used to extract one or more data itemsfrom the token stream or structure, where the extraction criteria areprocessed according to the organizing pattern to extract one or moretokens (or nodes from a layered structure). For position-based data, thetoken(s) at the position(s) identified by the extraction criteria areextracted. For attribute/value-based data, the token(s) and/or node(s)associated with the attribute(s) satisfying the extraction criteria areextracted. For hierarchical/layered data, the token(s) associated withthe node(s) matching the extraction criteria are extracted. Theextraction criteria may be as simple as an identifier string or may be aquery presented to a structured data repository (where the datarepository may be organized according to a database schema or dataformat, such as XML).

The extracted data may be used for further processing by the computingsystem. For example, the computing system of FIG. 10A, while performingone or more embodiments of the invention, may perform data comparison.Data comparison may be used to compare two or more data values (e.g., A,B). For example, one or more embodiments may determine whether A>B, A=B,A!=B, A<B, etc. The comparison may be performed by submitting A, B, andan opcode specifying an operation related to the comparison into anarithmetic logic unit (ALU) (i.e., circuitry that performs arithmeticand/or bitwise logical operations on the two data values). The ALUoutputs the numerical result of the operation and/or one or more statusflags related to the numerical result. For example, the status flags mayindicate whether the numerical result is a positive number, a negativenumber, zero, etc. By selecting the proper opcode and then reading thenumerical results and/or status flags, the comparison may be executed.For example, in order to determine if A>B, B may be subtracted from A(i.e., A−B), and the status flags may be read to determine if the resultis positive (i.e., if A>B, then A−B>0). In one or more embodiments, Bmay be considered a threshold, and A is deemed to satisfy the thresholdif A=B or if A>B, as determined using the ALU. In one or moreembodiments of the invention, A and B may be vectors, and comparing Awith B requires comparing the first element of vector A with the firstelement of vector B, the second element of vector A with the secondelement of vector B, etc. In one or more embodiments, if A and B arestrings, the binary values of the strings may be compared.

The computing system in FIG. 10A may implement and/or be connected to adata repository. For example, one type of data repository is a database.A database is a collection of information configured for ease of dataretrieval, modification, re-organization, and deletion. DatabaseManagement System (DBMS) is a software application that provides aninterface for users to define, create, query, update, or administerdatabases.

The user, or software application, may submit a statement or query intothe DBMS. Then the DBMS interprets the statement. The statement may be aselect statement to request information, update statement, createstatement, delete statement, etc. Moreover, the statement may includeparameters that specify data, or data container (database, table,record, column, view, etc.), identifier(s), conditions (comparisonoperators), functions (e.g. join, full join, count, average, etc.), sort(e.g. ascending, descending), or others. The DBMS may execute thestatement. For example, the DBMS may access a memory buffer, a referenceor index a file for read, write, deletion, or any combination thereof,for responding to the statement. The DBMS may load the data frompersistent or non-persistent storage and perform computations to respondto the query. The DBMS may return the result(s) to the user or softwareapplication.

The computing system of FIG. 10A may include functionality to presentraw and/or processed data, such as results of comparisons and otherprocessing. For example, presenting data may be accomplished throughvarious presenting methods. Specifically, data may be presented througha user interface provided by a computing device. The user interface mayinclude a GUI that displays information on a display device, such as acomputer monitor or a touchscreen on a handheld computer device. The GUImay include various GUI widgets that organize what data is shown as wellas how data is presented to a user. Furthermore, the GUI may presentdata directly to the user, e.g., data presented as actual data valuesthrough text, or rendered by the computing device into a visualrepresentation of the data, such as through visualizing a data model.

For example, a GUI may first obtain a notification from a softwareapplication requesting that a particular data object be presented withinthe GUI. Next, the GUI may determine a data object type associated withthe particular data object, e.g., by obtaining data from a dataattribute within the data object that identifies the data object type.Then, the GUI may determine any rules designated for displaying thatdata object type, e.g., rules specified by a software framework for adata object class or according to any local parameters defined by theGUI for presenting that data object type. Finally, the GUI may obtaindata values from the particular data object and render a visualrepresentation of the data values within a display device according tothe designated rules for that data object type.

Data may also be presented through various audio methods. In particular,data may be rendered into an audio format and presented as sound throughone or more speakers operably connected to a computing device.

Data may also be presented to a user through haptic methods. Forexample, haptic methods may include vibrations or other physical signalsgenerated by the computing system. For example, data may be presented toa user using a vibration generated by a handheld computer device with apredefined duration and intensity of the vibration to communicate thedata.

The above description of functions present only a few examples offunctions performed by the computing system of FIG. 10A and the nodesand/or client device in FIG. 10B. Other functions may be performed usingone or more embodiments of the invention.

FIG. 11 shows a schematic diagram of a system in accordance with one ormore embodiments. The system for selecting a protein target fortherapeutic application includes (i) a processing module (1104)including a computer processor (1106) configured to execute instructionsconfigured to: access genomic information (transcription/gene expressionanalysis, rare transcript, splice variant or fusion transcript on any ofthe present or future analytic platforms) associated with a patient,access PPI data from one or more reference human (academic, public orprivate) PPI networks, compute, using the genomic information and thePPI data, a thermodynamic or mathematical measure, and determine, fromthe thermodynamic or mathematical measure, a protein target within thePPI data; and (ii) a user device (1102) configured to present theprotein target to a user. The system may further include a datarepository (1110) configured to store the genomic information (1112) andthe PPI data (1114).

FIGS. 12A and 12B shows a flowchart of a method in accordance with oneor more embodiments. In one or more embodiments, the method as shown inFIGS. 12A and 12B is a computer-implemented method. Each step shown inFIGS. 12A and 12B are described together below.

In Step 1200, the omic data and PPI data are accessed. In one or moreembodiments, the omic data is the genomic information that is the RNA(e.g., mRNA, rRNA, tRNA, and other non-coding RNA) transcriptome value.In one or more embodiments, the PPI data is a PPI network, such as, butis not limited to, a human PPI network data comprising a network ofprotein nodes.

In one or more embodiments, the omic data and the PPI data can beobtained from at least one source including an academic database, apublic database, and a private database. In one or more embodiments, theomic data and the PPI data can be stored in a data repository.

In Step 1202, the omic data is overlaid onto the PPI data. In one ormore embodiments each protein node within network of the PPI data isassigned its respective omic data. Once the omic data has been overlaid,the log(2) transformed transcription data is first resealed to be in therange [0,1]. In one or more embodiments, the most highly, positivelyexpressed value will be set to 1.0 and the most negatively,down-regulated value will be set to 0.

It would be apparent to one of ordinary skill in the art that this iscomparable to stating that the most strongly up-regulated gene producesa protein of very great concentration, relative to the most stronglydown-regulated gene that will result in the lowest proteinconcentration.

In Step 1204, a thermodynamic measure for each of the protein nodeswithin the network of the PPI data is computed using the omic data. Inone or more embodiments, the thermodynamic measure of each protein nodeis the Gibbs free energy. The Gibbs free energy is computed for eachprotein node by applying the resealed value of each protein node intoEquation [1]. In one or more embodiments, the overall Gibbs free energyof the PPI data can be obtained using Equation [2].

In Step 1206, an energy landscape data corresponding to the network andthe thermodynamic measure is generated. In Step 1028, a PPI subnetworkis generated by applying a topological filtration to the energylandscape of the PPI data.

In one or more embodiments, the energy landscape contains a plurality ofenergy wells that are subnetworks of the PPI data. These PPI subnetworksare known as persistent homology. In one or more embodiments, theplurality of energy wells are also referred to as energetic subnetworksor Gibbs homology networks.

In one or more embodiments, the topological filtration is also referredto as a filtration threshold. The filtration threshold can be moved upfrom far below the lowest minima on an energy landscape. As thefiltration threshold is moved up further, small connected PPIsubnetworks, and later larger connected PPI subnetworks are revealed. Inone or more embodiments, the filtration threshold can be a value in arange of approximately 5 to 7000.

It would be apparent to one of ordinary skill in the art that when thefiltration threshold value is low, the complexity of the PPI subnetworkis also low. Similarly, when the filtration threshold value is high, thecomplexity of the PPI subnetwork is also high.

In Step 1210, a Betti number is computed for the generated PPIsubnetwork. In one or more embodiments, the Betti number of the PPIsubnetwork is computed based on the number of rings of four or moreproteins nodes within the PPI subnetwork. This Betti number is used as areference Betti number.

It would be apparent to one of ordinary skill in the art that as the PPIsubnetwork gets more complex, the Betti number of the PPI subnetworkwould also change. For example, a PPI subnetwork generated using afiltration threshold value of 10 may have a different Betti numbercompared to a PPI subnetwork generated using a filtration thresholdvalue of 1000.

In Step 1212, one or more protein nodes are sequentially removed fromthe PPI subnetwork. In one or more embodiments, when one or more proteinnodes are removed, the previously removed node(s) are replaced. In oneor more embodiments, the term “sequentially” is defined as following ina sequence. For example, the protein nodes in the PPI subnetwork areremoved in a predetermined sequence. This ensures that all of theprotein nodes in the PPI subnetwork are removed at least once.

In Step 1214, a Betti number for the PPI subnetwork is repetitivelycomputed each time one or more protein nodes are removed.

In Step 1216, a check is conducted to determine whether all of theprotein nodes within the PPI subnetwork have been removed at least once.If the result of the check is NO, then Steps 1212 and Steps 1214 arerepeated until all of the protein nodes in the PPI subnetwork have beenremoved at least once. If the result of the check is YES, then theprotein nodes and the respective Betti numbers are stored into an arrayin Step 1218.

In one or more embodiments, the array in Step 1218 maps each of theremoved protein node(s) to the respective Betti number computed for thePPI subnetwork with the protein node(s) removed.

In Step 1220, the recorded Betti numbers are compared to the referenceBetti number computed in Step 1210.

Based on the results of Step 1220, the protein node(s) that caused thelargest change in the Betti number is determined in Step 1222. In one ormore embodiments, the change in the Betti number represents an effectthat the protein node(s) has on a network complexity of the PPI data andthe removed protein node(s) that causes a highest drop of the networkcomplexity is the most significant protein target(s).

In one or more embodiments, the phrase “the most significant proteintarget(s)” is defined as the protein node(s) in a network or subnetworkthat causes the largest change in Betti number when removed. In otherwords the “most significant” protein target(s) is the number one proteintarget(s) of choice when administering drugs during therapy.

In Step 1224, a determination is made whether there are other PPIsubnetworks of interest. If the determination in Step 1224 results in aYES, the system returns to Step 1208 and applies a different filtrationthreshold value to the PPI data to obtain a different PPI subnetwork.Step 1210 to Step 1224 is then repeated for the new PPI subnetwork. Ifthe determination in Step 1224 results in a NO, the system proceeds toStep 1228 and displays the most significant protein node(s) of the PPIsubnetwork(s) to the user.

In one or more embodiments, when the complexity of the PPI subnetwork islow, removing any individual protein will drop the Betti number by thesame amount resulting in as many as eight or more equivalent targets. Incontrast, at high complexities, there is typically only one node thatleads to the biggest drop in Betti number. In one or more embodimentsthe filtration threshold is optimized by identifying the best targetsthrough a systematic application of thresholds between 8 and 128. Foreach threshold, the total Gibbs energy and the reference Betti numberfor each PPI subnetwork is computed. In one or more embodiments, thebest threshold is determined as 32.

While the invention has been described with respect to a limited numberof embodiments, those skilled in the art, having benefit of thisdisclosure, will appreciate that other embodiments can be devised whichdo not depart from the scope of the invention as disclosed herein.Accordingly, the scope of the invention should be limited only by theattached claims.

What is claimed is:
 1. A method to select a protein target fortherapeutic application, comprising: accessing genomic information andprotein-protein interaction (PPI) data, the PPI data comprising anetwork of protein nodes from at least one source; computing, using thegenomic information and the PPI data, a thermodynamic measure for eachprotein node within the network of protein nodes; generating an energylandscape data corresponding to the network of protein nodes and thethermodynamic measure; generating a PPI subnetwork by applying atopological filtration to the energy landscape data of the PPI data;computing a first Betti number for the PPI subnetwork; sequentiallyremoving a first protein node from the PPI subnetwork; computing asecond Betti number for the PPI subnetwork with the first protein noderemoved; computing a change between the first Betti number and thesecond Betti number; replacing the first protein node into the PPIsubnetwork; sequentially removing a second protein node from the PPIsubnetwork, wherein the second protein node is different from the firstprotein node; computing a third Betti number for the PPI subnetwork withthe second protein node removed and the first protein node replaced;computing a change between the first Betti number and the third Bettinumber; determining, based on the change between the first Betti numberand the second Betti number and the change between the first Bettinumber and the third Betti number, a most significant protein targetwithin the PPI subnetwork.
 2. The method of claim 1, further comprising:displaying the most significant protein target to a user.
 3. The methodof claim 1, further comprising: storing, in a data repository, thegenomic information and the PPI data.
 4. The method of claim 3, whereinthe at least one source is at least one selected from a group consistingof an academic database, a public database, and a private database. 5.The method of claim 3, wherein the genomic information is at least onetranscription data selected from a group consisting of messenger RNA(mRNA), RNA sequencing (RNA-seq), and Clustered regularly interspacedshort palindromic repeats (CRISPR).
 6. The method of claim 5, whereinthermodynamic measure is Gibbs free energy for each of the protein nodeswithin the PPI data is computed using the transcription data and anequation of: $G_{i} = {c_{i}\ln\frac{c_{i}}{\sum\limits_{j = i}c_{j}}}$and an overall Gibbs free energy of all of the protein nodes within thePPI data is computed using an equation of:${qG} = {\sum\limits_{i}G_{i}}$
 7. The method of claim 1, wherein thePPI subnetwork is a persistent homology that is extracted from theenergy landscape of the PPI data using the topological filtration basedon a user set threshold.
 8. The method of claim 7, wherein the user setthreshold is between 5 to
 7000. 9. The method of claim 1, wherein theBetti number of the PPI subnetwork is computed based on the number ofrings of four or more proteins nodes within the PPI subnetwork.
 10. Themethod of claim 1, wherein the Betti numbers and respective removedprotein nodes are stored in an array.
 11. The method of claim 1, whereinthe change in the Betti number represents an effect that the singleprotein node has on a network complexity of the PPI data and the singleremoved protein node that causes a highest drop of the networkcomplexity is the most significant protein target.
 12. A computingsystem that selects a protein target for therapeutic application,comprising: a processing circuitry configured to execute instructionsto: access genomic information and protein-protein interaction (PPI)data comprising a network of protein nodes from at least one source;compute, using the genomic information and the PPI data, a thermodynamicmeasure for each of the protein nodes within the network; generate anenergy landscape data corresponding to the network and the thermodynamicmeasure; generate a PPI subnetwork by applying a topological filtrationto the energy landscape of the PPI data; compute a first Betti numberfor the PPI subnetwork; sequentially remove a first protein node fromthe PPI subnetwork; compute a second Betti number for the PPI subnetworkwith the first protein node removed; compute a change between the firstBetti number and the second Betti number; replace the first protein nodeinto the PPI subnetwork; sequentially remove a second protein nodedifferent from the first protein node from the PPI subnetwork; compute athird Betti number for the PPI subnetwork with the second protein noderemoved and first protein node replaced; compute a change between thefirst Betti number and the third Betti number; and determine, based onthe change between the first Betti number and the second Betti numberand the change between the first Betti number and the third Bettinumber, a most significant protein target within the PPI subnetwork; anda display circuitry configured to execute instructions to display themost significant protein target to a user.
 13. The system of claim 12,further comprising: a data repository configured to store the genomicinformation and the PPI data.
 14. A non-transitory computer-readablemedium having instructions stored thereon that, in response to executionby the computer system, cause the computer system to perform operationscomprising: computing, using the genomic information and the PPI data, athermodynamic measure for each of the protein nodes within the network;generating an energy landscape data corresponding to the network and thethermodynamic measure; generating a PPI subnetwork by applying atopological filtration to the energy landscape of the PPI data;computing a first Betti number for the PPI subnetwork; sequentiallyremoving a first protein node from the PPI subnetwork; computing asecond Betti number for the PPI subnetwork with the first protein noderemoved; computing a change between the first Betti number and thesecond Betti number; replacing the first protein node into the PPIsubnetwork; sequentially removing a second protein node different fromthe first protein node from the PPI subnetwork; computing a third Bettinumber for the PPI subnetwork with the second protein node removed andfirst protein node replaced; computing a change between the first Bettinumber and the third Betti number; and determining, based on the changebetween the first Betti number and the second Betti number and thechange between the first Betti number and the third Betti number, a mostsignificant protein target within the PPI subnetwork.
 15. Thenon-transitory computer-readable medium of claim 14, whereininstructions stored thereon that, in response to execution by thecomputer system, cause the computer system to perform operations furthercomprising displaying the most significant protein target to a user.